Unreal Nature

February 23, 2013

Community Resource

Filed under: Uncategorized — unrealnature @ 6:52 am

… Conceptually, metagenomics implies that the communal gene pool is evolutionarily important and that genetic material can fruitfully be thought of as the community resource for a superorganism or metaorganism, rather than the exclusive property of individual organisms.

This is from Processes of Life: Essays in the Philosophy of Biology by John Dupré (2012). This particular chapter was co-written with Maureen O’Malley:

… Metagenomics — also called environmental genomics, community genomics, ecogenomics, or microbial population genomics — consists of the genome-based analysis of entire communities of complexly interacting organisms in diverse ecological contexts.

… Metagenomics has amplified insights into and questions about the genetic heterogeneity of populations and the genomic mosaicism of individuals. Understanding this genomic variability requires a deeper understanding of evolutionary processes and the mechanisms of genetic exchange and recombination. Metagenomics naturally aligns with an area of investigation that is sometimes called ‘horizontal genomics’ because both are concerned with the plethora of mobile genetic elements available to microbial communities and with the ways in which the metagenomic resources they inherit are shared and utilized.

The metagenomic role of gene cassettes provides an interesting example of how such study is being pursued. Gene cassettes are intergenomically mobile genes that are integrated into genomes in units called integrons. Such cassettes usually carry genes for environmental emergencies, such as antibiotic assaults on prokaryote communities, rather than genes for everyday function. Cassettes, and the integron elements in the host genome that allow the cassettes to be inserted and expressed (or excised), are efficient  mechanisms for the movement and expression of genes within and between species, and are implicated heavily in antibiotic resistance. Gene cassettes were originally studied individually but a metagenomic perspective allows them to be treated as a ‘floating’ evolutionary resource of high diversity and widespread activity that exists independent of individuals and is likely to have a high impact on bacterial genome evolution.

Although the extent, types, and precise effects on the metagenome of mobile resources (cassettes, as well as all the genetic material available for exchange to greater or lesser degrees by conjugation, transformation, and transduction) still require much more research, the conceptual implications for evolutionary understanding are already powerful, particularly because such studies back up extensive work done on lateral gene transfer and recombination processes. Metagenomic analysis supports and extends the earlier unexpected findings of comparative microbial genomics, which contradicted the dominant eukaryo-centric paradigm of vertical inheritance and mutation-driven species division that give rise to a single Tree of Life. Rather than focusing on individual organismal lineages, such metagenomic studies enable a shift in scientific and philosophical attention to an overall evolutionary process in which diverse and diversifying metagenomes underlie the differentiation of interactions within evolving and diverging ecosystems. Conceptually, metagenomics implies that the communal gene pool is evolutionarily important and that genetic material can fruitfully be thought of as the community resource for a superorganism or metaorganism, rather than the exclusive property of individual organisms.

[ … ]

… A final critical point about metaorganisms is that they are paradigmatically dynamic entities and therefore very clear illustrations of the ultimate necessity of a process-oriented approach to biological investigation. None of the entities that constitute organisms, or which organisms constitute, are static. Genomes, cells, and ecosystems are in constant interactive flux: subtly different in every iteration, but similar enough to constitute a distinctive process. The greatest significance of this point is perhaps that its appreciation will prevent us from taking too literally mechanistic models of biological processes. A good machine starts with all its parts precisely constructed to interact together in the way that will generate its intended functions. The technical manual for a car specifies exactly the ideal state of every single component. Though the parts of a machine are not unchanging, of course, their changes constitute a relentless, unidirectional trend towards failure. As friction, corrosion, and so on gradually transform these components from their ideal forms, the function of the car deteriorates. For a while these failing components can be replaced with replicas, close to the ideal types specified in the manual, but eventually too many parts will have deviated too far from the ideal, and the car will be abandoned, crushed, and recycled. No such unidirectional tendency towards failure characterizes biological processes: although perhaps all organisms die in the end, many exhibit high levels of stability for centuries and millenia.

… Analysing biological processes into things is necessarily to make an abstraction. Life is not composed in a machine-like way out of unchanging individual constituents. Genomes, cells, organisms, lineages are all assemblages of constantly changing entities in constant flux. Unlike the case of a machine, the stability of life processes is not maintained by the constant interactions of unchanging parts, but by dynamic, self-sustaining, and self-repairing processes. There is no doubt that mechanistic investigations of life processes have provided profound insights, and this very fact is enough to show that quasi-mechanistic elements are fundamental constituents of life processes. But there are limits to how far conventional mechanistic investigations can take us in understanding the dynamic stability of processes at this hierarchy of different levels. Such understanding will require models that incorporate both the capacities provided by mechanistic or quasi-mechanistic constituents, and the constraints and causal influences provided by properties of the wider systems of which these constituents are parts.

My most recent previous post from Dupré’s book is here.





  1. We live in exciting times, don’t we?

    Seriously: I’m amazed at the world I’ve been privileged to stumble upon in my lifetime. I was born just late enough to navigate it but just early enough to experience its birth … what greater adventure could there be?

    That astonishing good fortune applies even in mundane practical aspects of my own environment … digital photography, for instance, arrived at a time when I had learnt so much craft from wet silver days that could still be utilised, and hadn’t yet been forgotten – young students now don’t get that advantage to twin with all the wonderful new opportunities, it’s a narrow temporal window.

    And, of course, the web has brought be the opportunity which never used to exist: for you (whom I would never have previously met) to stimulate my intellect with you insights onto and into material which I have myself missed.

    “O brave new world,
    That has such people in‘t!”

    (OK, so that makes me Caliban; endaxi, I can live with it [grin])

    Comment by Felix — February 23, 2013 @ 3:43 pm

  2. Of course we live in exciting times! We love our personal WAP … [ <<< no cheerful comment goes unpunished]

    Comment by unrealnature — February 24, 2013 @ 6:56 am

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